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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $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' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ), 'gf_id' => 'HOM05D001649', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001649' ), 'data_identifier' => 'HOM05D001649', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001649', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '392', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p23090' => 'bna', 'A03p16030' => 'bna', 'A03p55960' => 'bna', 'A04p33920' => 'bna', 'Aa31LG1G27080' => 'aar', 'Aa31LG3G8220' => 'aar', 'Aa31LG4G1180' => 'aar', 'Aa31sc16G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3596' => 'aag', 'Actinidia03092' => 'ach', 'Actinidia03093' => 'ach', 'Actinidia08943' => 'ach', 'Actinidia09571' => 'ach', 'Actinidia14210' => 'ach', 'Actinidia14211' => 'ach', 'Actinidia28381' => 'ach', 'Actinidia31442' => 'ach', 'Actinidia32917' => 'ach', 'Actinidia36873' => 'ach', 'Ah.05g175500' => 'amhyb', 'Ah.07g208520' => 'amhyb', 'Ah.13g076660' => 'amhyb', 'AL2G40510' => 'aly', 'AL4G44760' => 'aly', 'AL7G27740' => 'aly', 'AL8G26060' => 'aly', 'Aqoxy7G00519' => 'aox', 'Aqoxy7G03395' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6X863X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BU858T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ2RGS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I81MIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEF8WS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RBWH0U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W1M1TV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WHVZ2S' => 'arhy', 'AT1G80870' => 'ath', 'AT2G45590' => 'ath', 'AT4G25390' => 'ath', 'AT5G51770' => 'ath', 'ATR0580G257' => 'atr', 'ATR0661G458' => 'atr', 'Atru.chr1.2795' => 'acertr', 'Atru.chr1.589' => 'acertr', 'Atru.chr1.590' => 'acertr', 'Atru.chr5.358' => 'acertr', 'AUR62016074' => 'cqu', 'AUR62021283' => 'cqu', 'AUR62026151' => 'cqu', 'AUR62030385' => 'cqu', 'BcaB01g04156' => 'bca', 'BcaB05g25220' => 'bca', 'BcaB06g29412' => 'bca', 'BcaC01g06138' => 'bca', 'BcaC02g07080' => 'bca', 'BcaC03g15922' => 'bca', 'BcaC06g32814' => 'bca', 'BolC2t09696H' => 'bol', 'BolC3t14277H' => 'bol', 'BolC4t28672H' => 'bol', 'BolC7t45913H' => 'bol', 'BraA02t07307Z' => 'bra', 'BraA03t10894Z' => 'bra', 'BraA03t14668Z' => 'bra', 'BraA04t18853Z' => 'bra', 'C02p36850' => 'bna', 'C03p18860' => 'bna', 'C04p71730' => 'bna', 'C07p54270' => 'bna', 'CAN.G1283.3' => 'can', 'CAN.G1561.13' => 'can', 'CAN.G407.6' => 'can', 'CANSAT56G1648' => 'cansat', 'CANSAT56G3690' => 'cansat', 'CANSAT80G1926' => 'cansat', 'CARHR073600' => 'chi', 'CARHR140810' => 'chi', 'CARHR232800' => 'chi', 'CARHR264650' => 'chi', 'Carub.0002s2666' => 'cru', 'Carub.0004s2823' => 'cru', 'Carub.0007s1562' => 'cru', 'Carub.0008s1179' => 'cru', 'Ca_01009_v3' => 'car', 'Ca_10825_v3' => 'car', 'Ca_19539_v3' => 'car', 'Ca_23819_v3' => 'car', 'Cc02_g03680' => 'ccan', 'Cc02_g36360' => 'ccan', 'Cc04_g05170' => 'ccan', 'CDE02G1199' => 'cde', 'CDE02G1614' => 'cde', 'CDE02G2657' => 'cde', 'CDE02G3712' => 'cde', 'CDE02G3927' => 'cde', 'Cfa001831' => 'cfa', 'Cfa001875' => 'cfa', 'Cfa008250' => 'cfa', 'Ciclev10004535m.g' => 'ccl', 'Ciclev10019199m.g' => 'ccl', 'Ciclev10025505m.g' => 'ccl', 'CiPaw.01G255200' => 'cil', 'CiPaw.01G259500' => 'cil', 'CiPaw.02G162600' => 'cil', 'CiPaw.02G165200' => 'cil', 'CiPaw.03G098800' => 'cil', 'CiPaw.14G085100' => 'cil', 'ClCG06G000260' => 'cla', 'ClCG09G003360' => 'cla', 'COL.COLO4_08467' => 'col', 'COL.COLO4_12593' => 'col', 'COL.COLO4_14214' => 'col', 'COL.COLO4_26735' => 'col', 'Cpa.g.c40487' => 'cpa', 'Cpa.g.sc18.157' => 'cpa', 'Cpa.g.sc3.519' => 'cpa', 'CsaV3_3G016550' => 'csa', 'CsaV3_6G006050' => 'csa', 'CsaV3_7G031870' => 'csa', 'CSS0003363' => 'camsi', 'CSS0009486' => 'camsi', 'CSS0048703' => 'camsi', 'CSS0049744' => 'camsi', 'DCAR_006885' => 'dca', 'DCAR_009412' => 'dca', 'DCAR_018137' => 'dca', 'DCAR_021371' => 'dca', 'Dinv21414' => 'din', 'Dinv28515' => 'din', 'Dinv32400' => 'din', 'Duzib068G1169' => 'dzi', 'Duzib138G1951' => 'dzi', 'Duzib192G0428' => 'dzi', 'Duzib235G1229' => 'dzi', 'ECA236G2921' => 'eca', 'ECA247G1734' => 'eca', 'ECA248G3849' => 'eca', 'EL10Ac3g05758' => 'bvu', 'EL10Ac3g07178' => 'bvu', 'Eucgr.E01348' => 'egr', 'Eucgr.F03967' => 'egr', 'Eucgr.K00180' => 'egr', 'FAN01G0326' => 'fan', 'FAN01G3151' => 'fan', 'FAN02G1559' => 'fan', 'FAN03G0865' => 'fan', 'FAN03G2171' => 'fan', 'FAN03G3400' => 'fan', 'FAN05G2393' => 'fan', 'FAN06G1950' => 'fan', 'FAN06G2316' => 'fan', 'FAN06G2708' => 'fan', 'FAN06G3646' => 'fan', 'FAN10G1360' => 'fan', 'FAN10G1952' => 'fan', 'FAN10G2318' => 'fan', 'FAN10G3321' => 'fan', 'FAN10G4136' => 'fan', 'FAN14G4627' => 'fan', 'FAN20G1064' => 'fan', 'FvH4_6g28550' => 'fve', 'FvH4_7g12490' => 'fve', 'FvH4_7g28580' => 'fve', 'Glyma.03G020700' => 'gma', 'Glyma.07G082600' => 'gma', 'Glyma.09G150100' => 'gma', 'Glyma.10G241500' => 'gma', 'Glyma.13G370700' => 'gma', 'Glyma.15G002900' => 'gma', 'Glyma.16G201500' => 'gma', 'Glyma.20G152800' => 'gma', 'Gohir.A05G118600' => 'ghi', 'Gohir.A09G043200' => 'ghi', 'Gohir.A11G083100' => 'ghi', 'Gohir.A12G263000' => 'ghi', 'Gohir.D05G119500' => 'ghi', 'Gohir.D09G044600' => 'ghi', 'Gohir.D11G087200' => 'ghi', 'Gohir.D12G263500' => 'ghi', 'Gorai.006G066000' => 'gra', 'Gorai.007G093100' => 'gra', 'Gorai.008G282500' => 'gra', 'Gorai.009G123100' => 'gra', 'GSVIVG01015977001' => 'vvi', 'GSVIVG01018462001' => 'vvi', 'GSVIVG01027564001' => 'vvi', 'HanXRQChr02g0033971' => 'han', 'HanXRQChr06g0169251' => 'han', 'HanXRQChr07g0206711' => 'han', 'HanXRQChr14g0461871' => 'han', 'Haze_13801' => 'cav', 'Haze_16673' => 'cav', 'Haze_16724' => 'cav', 'Hma1.2p1_0012F.1_g007780' => 'hma', 'Hma1.2p1_0099F.1_g048790' => 'hma', 'Hma1.2p1_0329F.1_g127120' => 'hma', 'Hma1.2p1_0329F.1_g127130' => 'hma', 'HPP92_001550' => 'vpl', 'HPP92_003299' => 'vpl', 'HPP92_003734' => 'vpl', 'HPP92_003760' => 'vpl', 'Hund11786' => 'sun', 'Lalb_Chr00c36g0408881' => 'lal', 'Lalb_Chr00c36g0408891' => 'lal', 'Lalb_Chr00c36g0408901' => 'lal', 'Lalb_Chr01g0008901' => 'lal', 'Lalb_Chr02g0140831' => 'lal', 'Lalb_Chr03g0032971' => 'lal', 'Lalb_Chr07g0189541' => 'lal', 'Lalb_Chr24g0392841' => 'lal', 'Lj1A986T54' => 'lonja', 'Lj2g0005098' => 'lja', 'Lj3g0002144' => 'lja', 'Lj3g0003838' => 'lja', 'Lj3g0027358' => 'lja', 'Lj5g0023907' => 'lja', 'Lj9C573T7' => 'lonja', 'Lj9P492T30' => 'lonja', 'Lsat_1_v5_gn_1_110440' => 'lsa', 'Lsat_1_v5_gn_1_30941' => 'lsa', 'Lsat_1_v5_gn_2_130000' => 'lsa', 'Lsat_1_v5_gn_4_93861' => 'lsa', 'Lsat_1_v5_gn_6_2160' => 'lsa', 'Lsat_1_v5_gn_7_6720' => 'lsa', 'Manes.04G102100' => 'mes', 'Manes.05G043100' => 'mes', 'Manes.06G140400' => 'mes', 'Manes.11G067000' => 'mes', 'Mapoly0140s0042' => 'mpo', 'MBI14_g34254_MAGBIO' => 'mbi', 'MD02G1198700' => 'mdo', 'MD12G1112300' => 'mdo', 'MD17G1223700' => 'mdo', 'Medtr0007s0390' => 'mtr', 'Medtr1g102360' => 'mtr', 'Medtr2g105260' => 'mtr', 'Medtr8g035560' => 'mtr', 'MELO3C006853.2' => 'cme', 'MELO3C022512.2' => 'cme', 'MELO3C023470.2' => 'cme', 'Migut.B01661' => 'egut', 'Migut.D01127' => 'egut', 'Migut.F00406' => 'egut', 'MSTRG.20772' => 'ama', 'MSTRG.27156' => 'ama', 'MSTRG.4676' => 'ama', 'MSTRG.8786' => 'ama', 'MSTRG.9400' => 'ama', 'Nitab4.5_0000072g0030' => 'nta', 'Nitab4.5_0001757g0010' => 'nta', 'Nitab4.5_0002436g0080' => 'nta', 'Nitab4.5_0002700g0170' => 'nta', 'Nitab4.5_0003739g0030' => 'nta', 'Nitab4.5_0005340g0010' => 'nta', 'Nitab4.5_0009867g0030' => 'nta', 'Nn1g01149' => 'nnu', 'Nn1g03629' => 'nnu', 'Nn1g08967' => 'nnu', 'Nn2g12396' => 'nnu', 'Nn3g21151' => 'nnu', 'Nn6g34342' => 'nnu', 'Nn8g39908' => 'nnu', 'Oeu009805.1' => 'oeu', 'Oeu022524.1' => 'oeu', 'Oeu026239.1' => 'oeu', 'Oeu030153.1' => 'oeu', 'Oeu039229.2' => 'oeu', 'Oeu042592.2' => 'oeu', 'Oeu051575.1' => 'oeu', 'Os03g0251700' => 'osa', 'Os08g0275200' => 'osa', 'Os10g0187500' => 'osa', 'Peaxi162Scf00192g00719' => 'pax', 'Peaxi162Scf00553g00521' => 'pax', 'Peaxi162Scf00988g00033' => 'pax', 'PGR042G2386' => 'pgr', 'PGR102G0063' => 'pgr', 'PGR142G1763' => 'pgr', 'PGSC0003DMG400000140' => 'stu', 'PGSC0003DMG400007560' => 'stu', 'PGSC0003DMG400014150' => 'stu', 'Phvul.004G124400' => 'pvu', 'Phvul.005G182900' => 'pvu', 'Phvul.007G064200' => 'pvu', 'Phvul.010G086600' => 'pvu', 'Potri.001G043700' => 'ptr', 'Potri.002G150800' => 'ptr', 'Potri.003G183100' => 'ptr', 'Potri.012G131900' => 'ptr', 'Potri.014G072900' => 'ptr', 'Potri.015G134100' => 'ptr', 'Pp3c13_4530' => 'ppa', 'Pp3c3_8250' => 'ppa', 'Prupe.2G149500' => 'ppe', 'Prupe.2G285800' => 'ppe', 'Prupe.3G099300' => 'ppe', 'Psat0s148g0080' => 'psa', 'Psat4g150400' => 'psa', 'Psat5g306760' => 'psa', 'Psat6g203640' => 'psa', 'PSO063G5238' => 'pso', 'PSO478G0436' => 'pso', 'PSO782G1606' => 'pso', 'PSO782G1909' => 'pso', 'QL05p035679' => 'qlo', 'QL08p050988' => 'qlo', 'QL08p051566' => 'qlo', 'QL12p039040' => 'qlo', 'RcHm_v2.0_Chr1g0351331' => 'rch', 'RcHm_v2.0_Chr1g0375991' => 'rch', 'RcHm_v2.0_Chr2g0132871' => 'rch', 'Rhsim03G0173600' => 'rsi', 'Rhsim07G0024000' => 'rsi', 'Rhsim09G0194700' => 'rsi', 'Rhsim12G0187200' => 'rsi', 'Sabra01G0030100' => 'sbr', 'Sabra02G0119200' => 'sbr', 'Sabra03G0133700' => 'sbr', 'Sabra12G0099200' => 'sbr', 'Sabra14G0052100' => 'sbr', 'Sabra15G0146300' => 'sbr', 'SalBow4G0027' => 'sbo', 'SalBow4G0996' => 'sbo', 'SalBow4G1459' => 'sbo', 'SalBow7G1676' => 'sbo', 'SalBow7G4433' => 'sbo', 'Sc02g0002380' => 'sci', 'Sc10g0005330' => 'sci', 'Sc25g0000240' => 'sci', 'Sed0005069' => 'sed', 'Sed0007174' => 'sed', 'Sed0009734' => 'sed', 'Sed0012900' => 'sed', 'Sed0014449' => 'sed', 'SEGI_01592' => 'sgi', 'SEGI_15726' => 'sgi', 'SEGI_22995' => 'sgi', 'SEGI_25870' => 'sgi', 'SEGI_29870' => 'sgi', 'SGA_v2.0_scaffold221G42749' => 'sas', 'SGA_v2.0_scaffold26G11302' => 'sas', 'SGA_v2.0_scaffold2G01103' => 'sas', 'SGA_v2.0_scaffold403G51005' => 'sas', 'SGA_v2.0_scaffold95G28884' => 'sas', 'SHI11290' => 'shi', 'SHI13844' => 'shi', 'SMO197G0044' => 'smo', 'SMO239G0032' => 'smo', 'SMO364G0883' => 'smo', 'Solyc01g094020.3' => 'sly', 'Solyc03g006920.2' => 'sly', 'Solyc03g117550.1' => 'sly', 'Sopen01g037840' => 'spe', 'Sopen03g002920' => 'spe', 'Sopen03g036460' => 'spe', 'Sp4g27640' => 'spa', 'Sp5g34870' => 'spa', 'Sp6g13990' => 'spa', 'Sp7g23410' => 'spa', 'TAR374G0534' => 'tar', 'TAR375G0908' => 'tar', 'TAR625G0792' => 'tar', 'TAR636G2238' => 'tar', 'TAR636G3438' => 'tar', 'THA.LOC104811501' => 'tha', 'THA.LOC104817262' => 'tha', 'Thecc.01G372500' => 'tca', 'Thecc.03G165600' => 'tca', 'Thecc.06G042500' => 'tca', 'Thhalv10001343m.g' => 'esa', 'Thhalv10015950m.g' => 'esa', 'Thhalv10018204m.g' => 'esa', 'TPR.G17406' => 'tpr', 'TPR.G26591' => 'tpr', 'TPR.G30882' => 'tpr', 'TPR.G7377' => 'tpr', 'TWI12G1116' => 'twi', 'TWI18G0232' => 'twi', 'TWI23G1008' => 'twi', 'TWI23G1067' => 'twi', 'TWI59G0625' => 'twi', 'vmacro09875' => 'vma', 'vmacro13367' => 'vma', 'vmacro22938' => 'vma', 'VMungo0331G0090' => 'vmu', 'VMungo0331G1141' => 'vmu', 'VMungo0464G2110' => 'vmu', 'VMungo0720G1306' => 'vmu', 'VMungo1080G0061' => 'vmu', 'VMungo1080G1363' => 'vmu', 'Zm00001eb010820' => 'zma', 'Zm00001eb412320' => 'zma' ) $gf_id = 'HOM05D001649' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001649' ) $data_identifier = 'HOM05D001649' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 7, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412320' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1